Biology subjects

Mattila, T.

Publications and source records attributed to Mattila, T..

3 recordsLinked to original sources

bioRxiv2026

Operationalising the context in regenerative agriculture: decision-making and farm variability

Soil degradation is a widespread challenge that requires a broad response at the individual farm level. To ensure effectivity, the practices should be tailored to the farm context: land manager objectives and farm specific challenges. These have however been difficult to quantify. Here we demonstrate that a workable farm context can be created based on a value survey, open satellite and soil data, and published models for vegetation gross primary productivity and soil erosion. Based on the findings, despite individual differences, farmers value profitability and operational efficiency, but also biodiversity and soil health. At least the regenerative farmers surveyed also value working for the greater good more than maintaining tradition or power. In spite of wide differences in farm production orientation, we also found that each farm also had a broad variation in individual fields GPP. Most fields have a stable GPP level, which is either high or low, and that there is a 2-3-fold difference between the weakest and best producing fields indicating the potential for improving GPP by improving the growing conditions on currently weak fields. In addition, soil loss was found to be highly concentrated in critical source areas, where 10% of the field area contributed to 50% of the soil loss. Overall, open data can be linked to modelling workflows to rapidly produce a decision-making context for farmers. This facilitates benchmarking and co-learning as well as enables land managers and advisors to identify the farm context for planning effective responses to soil degradation.

ecology↗

bioRxiv2026

A Global Genomic Resource for Outcrossing Arabidopsis lyrata and Arabidopsis arenosa

Genetic studies leveraging natural variation in Arabidopsis species have improved our understanding of evolutionary genetic processes underlying ecologically important and adaptive traits. Integrating the thorough functional knowledge accumulated in A. thaliana with the extensive natural variation in outcrossing Arabidopsis species is a powerful approach to study the basis of adaptation in natural evolutionary and ecological contexts. Here we present an integrated genomics database of sequenced genomes from several studies in A. lyrata (1018 genomes in total) and A. arenosa (736 genomes in total), spanning the geographic ranges of these two ploidy-variable, outcrossing taxa. We provide a searchable genome browser with population data mapped to respective reference genomes, an interactive geographic map of population structure clusters, and an efficient way to subsample the full dataset of genetic variation, available at arabidopsislyrata.org. To demonstrate its utility, we perform a genome-wide association study on a latitudinal cline of A. lyrata and find strong associations of several loci with latitude, including variants in key regulators of photoperiodic growth. This resource provides access to genetic diversity data in a single repository, enabling further studies of comparative genetics and local adaptation, as well as of individual genes of interest.

evolutionary biology↗

bioRxiv2018

Utilization of tissue ploidy level variation in de novo transcriptome assembly of Pinus sylvestris

Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies, including the utility of haploid (megagametophyte) tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.

evolutionary biology↗